Objective. Clinical outcome of Helicobacter pylori (H. pylori) infection might be associated with specific virulence-associated bacterial genotypes. The distribution of different bacterial genotypes varies geographically. The aim of this study was to assess the relationship between cagPAI, vacA, and iceA status and severity of the disease in patients from Lithuania, infected by H. pylori. Material and methods. H. pylori from 81 patients (37 with duodenal ulcer and 44 with chronic gastritis) was isolated from gastric biopsy specimens and cultured. Bacterial genotypes cagPAI, vacA (s and m subtypes) and iceA were analyzed by polymerase chain reaction using specific primers. Results. The cagPAI was identified in 59.3% of Lithuanian H. pylori strains investigated. H. pylori strains cultured from duodenal ulcer (DU) patients more frequently (PP0.05). Conclusion. Our study suggests that cagPAI and vacA s1 genotypes are associated with peptic ulceration in Lithuanian patients infected by H. pylori.